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Brynjar was born in Reykjavík and started his career with local club KR, playing three seasons with their senior squad. Brynjar moved to Norway in 1998 to play for Vålerenga and Moss FK before joining Swedish club Örgryte IS in 1999. After a season at the Gamla Ullevi English club Stoke City paid a club-record fee of £600,000 for Brynjar, with him becoming one of a number of Scandinavian players at Stoke following a take over by a group of Icelandic businessmen. He played 30 times for Stoke 1999–2000 as Stoke lost to Gillingham in the play-offs. He did play in the 2000 Football League Trophy Final as Stoke beat 2–1.[1] In 2000–01 Brynjar missed just three matches as Stoke again failed in the play-offs this time to Walsall but Brynjar did win the player of the year. He struggled with injury in 2001–02 as Stoke gained promotion by beating Brentford 2–0 in the play-off final. He played in 45 games in 2002–03 as Stoke narrowly avoided relegation and at the end of the season he left for Nottingham Forest on a free transfer.[2]

He failed to make much of an impact at Forest and after making 14 appearances he re-joined Stoke on a short-term loan.[3] He played three times for Stoke in 2003–04 until he was released by Forest at the end of the season.[4]

Brynjar signed for Watford in the summer of 2004, after being released by Forest.[5] He made 43 appearances in an impressive first season. However, Ray Lewington's replacement as Watford manager, Adrian Boothroyd, to some raised eyebrows from the Watford support, allowed Brynjar to leave for Reading for a nominal fee in the summer of 2005.[6] He helped Reading win the Championship title in 2005–06 and stay in the Premier League in 2006–07 however relegation was suffered in 2007–08.[7] He slowly drifted in and out of the Reading side and left the club having made 163 appearances for the club scoring ten goals.

Brynjar moved to KR again after about 15 years abroad in March 2013.[8] After a season in which Brynjar helped KR win the league he retired as a player to become the assistant manager at fellow Úrvalsdeild outfit Stjarnan.[9][10]